A steepest descent calculation of RNA pseudoknots

We enumerate possible topologies of pseudoknots in single-stranded RNA molecules. We use a steepest-descent approximation in the large N matrix field theory, and a Feynman diagram formalism to describe the resulting pseudoknot structure

Enumeration of RNA structures by Matrix Models

We enumerate the number of RNA contact structures according to their genus, i.e. the topological character of their pseudoknots. By using a recently proposed matrix model formulation for the RNA folding problem, we obtain exact results for the simple case of an RNA molecule with an infinitely flexible backbone, in which any arbitrary pair of bases is allowed. We analyze the distribution of the genus of pseudoknots as a function of the total number of nucleotides along the phosphate-sugar backbone.Comment: RevTeX, 4 pages, 2 figure

New model for the neutrino mass matrix

I suggest a model based on a softly broken symmetry L_e - L_mu - L_tau and on Babu's mechanism for two-loops radiative generation of the neutrino masses. The model predicts that one of the physical neutrinos (nu_3) is massless and that its component along the nu_e direction (U_e3) is zero. Moreover, if the soft-breaking term is assumed to be very small, then the vacuum oscillations of nu_e have almost maximal amplitude and solve the solar-neutrino problem. New scalars are predicted in the 10 TeV energy range, and a breakdown of e-mu-tau universality should not be far from existing experimental bounds.Comment: 7 pages including 3 figure

A Model for Neutrino Masses and Dark Matter

We propose a model for neutrino masses that simultaneously results in a new dark matter candidate, the right-handed neutrino. We derive the dark matter abundance in this model, show how the hierarchy of neutrino masses is obtained, and verify that the model is compatible with existing experimental results. The model provides an economical method of unifying two seemingly separate puzzles in contemporary particle physics and cosmology.Comment: 4 pages, submitted to PR

Temperature effects on the magnetization of quasi-one-dimensional Peierls distorted materials

It is shown that temperature acts to disrupt the magnetization of Peierls distorted quasi-one-dimensional materials (Q1DM). The mean-field finite temperature phase diagram for the field theory model employed is obtained by considering both homogeneous and inhomogeneous condensates. The tricritical points of the second order transition lines of the gap parameter and magnetization are explicitly calculated. It is also shown that in the absence of an external static magnetic field the magnetization is always zero, at any temperature. As expected, temperature does not induce any magnetization effect on Peierls distorted Q1DM.Comment: 11 pages, 2 figure

Global turnover of histone post-translational modifications and variants in human cells

<p>Abstract</p> <p>Background</p> <p>Post-translational modifications (PTMs) on the N-terminal tails of histones and histone variants regulate distinct transcriptional states and nuclear events. Whereas the functional effects of specific PTMs are the current subject of intense investigation, most studies characterize histone PTMs/variants in a non-temporal fashion and very few studies have reported kinetic information about these histone forms. Previous studies have used radiolabeling, fluorescence microscopy and chromatin immunoprecipitation to determine rates of histone turnover, and have found interesting correlations between increased turnover and increased gene expression. Therefore, histone turnover is an understudied yet potentially important parameter that may contribute to epigenetic regulation. Understanding turnover in the context of histone modifications and sequence variants could provide valuable additional insight into the function of histone replacement.</p> <p>Results</p> <p>In this study, we measured the metabolic rate of labeled isotope incorporation into the histone proteins of HeLa cells by combining stable isotope labeling of amino acids in cell culture (SILAC) pulse experiments with quantitative mass spectrometry-based proteomics. In general, we found that most core histones have similar turnover rates, with the exception of the H2A variants, which exhibit a wider range of rates, potentially consistent with their epigenetic function. In addition, acetylated histones have a significantly faster turnover compared with general histone protein and methylated histones, although these rates vary considerably, depending on the site and overall degree of methylation. Histones containing transcriptionally active marks have been consistently found to have faster turnover rates than histones containing silent marks. Interestingly, the presence of both active and silent marks on the same peptide resulted in a slower turnover rate than either mark alone on that same peptide. Lastly, we observed little difference in the turnover between nearly all modified forms of the H3.1, H3.2 and H3.3 variants, with the notable exception that H3.2K36me2 has a faster turnover than this mark on the other H3 variants.</p> <p>Conclusions</p> <p>Quantitative proteomics provides complementary insight to previous work aimed at quantitatively measuring histone turnover, and our results suggest that turnover rates are dependent upon site-specific post-translational modifications and sequence variants.</p

Neutrino Masses and A TeV Scale Seesaw Mechanism

A simple extension of the Standard Model providing TeV scale seesaw mechanism is presented. Beside the Standard Model particles and right-handed Majorana neutrinos, the model contains a singly charged scalar, an extra Higgs doublet and three vector like singly charged fermions. In our model, Dirac neutrino mass matrix raises only at the loop level. Small but non-zero Majorana neutrino masses come from integrating out heavy Majorana neutrinos, which can be at the TeV scale. The phenomenologies of the model are investigated, including scalar mass spectrum, neutrino masses and mixings, lepton flavor violations, heavy neutrino magnetic moments as well as possible collider signatures of the model at the LHC.Comment: 13 pages, 4 figures. references adde

Brane Effects on Extra Dimensional Scenarios: A Tale of Two Gravitons

We analyze the propagation of a scalar field in multidimensional theories which include kinetic corrections in the brane, as a prototype for gravitational interactions in a four dimensional brane located in a (nearly) flat extra dimensional bulk. We regularize the theory by introducing an infrared cutoff given by the size of the extra dimensions and a physical ultraviolet cutoff of the order of the fundamental Planck scale in the higher dimensional theory. We show that, contrary to recent suggestions, the radius of the extra dimensions cannot be arbitrarily large. Moreover, for finite radii, the gravitational effects localized on the brane can substantially alter the phenomenology of collider and/or table-top gravitational experiments. This phenomenology is dictated by the presence of a massless graviton, with standard couplings to the matter fields, and a massive graviton which couples to matter in a much stronger way. While graviton KK modes lighter than the massive graviton couple to matter in a standard way, the couplings to matter of the heavier KK modes are strongly suppressed.Comment: 21 pages, latex2e, axodraw.sty, 2 figure

Hopping between Random Locations: Spectrum and Instanton

Euclidean random matrices appear in a broad class of physical problems involving disorder. The problem of determining their spectra can be mapped, using the replica method, into the study of a scalar field theory with an interaction of the type e^(psi^2). We apply the instanton method to study their spectral tails.Comment: 9 pages, Revtex, 2 postscript figure